3D-DART

3D-DART generates 3D-structural DNA models with defined conformations by providing control over both 'global' and 'local' conformational features.

Key Features:

• Global conformational control: The server enables users to define overall DNA structural parameters.
• Local conformational control: The server enables users to specify base-pair level structural features.
• Custom conformation generation: The server generates DNA-structural models in user-specified custom conformations.

Scientific Applications:

• Homology modeling templates: Generated DNA models serve as templates for homology modeling.
• Macro-molecular docking: Generated DNA models serve as starting structures for macro-molecular docking.
• NMR structure calculations: Generated DNA models serve as scaffolds for NMR structure calculations.
• Structural studies of DNA plasticity: Models reflect the intrinsic conformational adaptability of DNA when binding to proteins.

Methodology:

The computational engine uses the 3DNA software suite together with a collection of home-written python scripts.